Mercurial > repos > iuc > bbtools_bbmap

comparison bbmap.xml @ 6:c7a39190a385 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95
author iuc
date Tue, 05 Jul 2022 13:04:34 +0000
parents 6af1021d16a4
children 3fa2af3231df
comparison
equal deleted inserted replaced
5:6af1021d16a4 6:c7a39190a385
135 renamebyinsert='$output_options.renamebyinsert' 135 renamebyinsert='$output_options.renamebyinsert'
136 #if str($output_options.output_sort) == 'coordinate': 136 #if str($output_options.output_sort) == 'coordinate':
137 out='all_reads.bam' 137 out='all_reads.bam'
138 outu='unmapped_reads.bam' 138 outu='unmapped_reads.bam'
139 outm='mapped_reads.bam' 139 outm='mapped_reads.bam'
140 && samtools sort -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_all_reads' 'all_reads.bam' 140 && samtools sort --no-PG -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_all_reads' 'all_reads.bam'
141 && samtools sort -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_unmapped_reads' 'unmapped_reads.bam' 141 && samtools sort --no-PG -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_unmapped_reads' 'unmapped_reads.bam'
142 && samtools sort -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_mapped_reads' 'mapped_reads.bam' 142 && samtools sort --no-PG -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_mapped_reads' 'mapped_reads.bam'
143 #elif str($output_options.output_sort) == 'name': 143 #elif str($output_options.output_sort) == 'name':
144 out='all_reads.bam' 144 out='all_reads.bam'
145 outu='unmapped_reads.bam' 145 outu='unmapped_reads.bam'
146 outm='mapped_reads.bam' 146 outm='mapped_reads.bam'
147 && samtools sort -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_all_reads' 'all_reads.bam' 147 && samtools sort --no-PG -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_all_reads' 'all_reads.bam'
148 && samtools sort -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_unmapped_reads' 'unmapped_reads.bam' 148 && samtools sort --no-PG -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_unmapped_reads' 'unmapped_reads.bam'
149 && samtools sort -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_mapped_reads' 'mapped_reads.bam' 149 && samtools sort --no-PG -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_mapped_reads' 'mapped_reads.bam'
150 #else: 150 #else:
151 out='all_reads.bam' 151 out='all_reads.bam'
152 outu='unmapped_reads.bam' 152 outu='unmapped_reads.bam'
153 outm='mapped_reads.bam' 153 outm='mapped_reads.bam'
154 && mv 'all_reads.bam' '$output_all_reads' 154 && mv 'all_reads.bam' '$output_all_reads'
267 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/> 267 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
268 <param name="output_sort" value="coordinate"/> 268 <param name="output_sort" value="coordinate"/>
269 <output name="output_all_reads" ftype="bam"> 269 <output name="output_all_reads" ftype="bam">
270 <metadata name="dbkey" value="89"/> 270 <metadata name="dbkey" value="89"/>
271 <assert_contents> 271 <assert_contents>
272 <has_size value="9433" delta="300"/> 272 <has_size value="9639" delta="300"/>
273 </assert_contents> 273 </assert_contents>
274 </output> 274 </output>
275 <output name="output_unmapped_reads" ftype="bam"> 275 <output name="output_unmapped_reads" ftype="bam">
276 <metadata name="dbkey" value="89"/> 276 <metadata name="dbkey" value="89"/>
277 <assert_contents> 277 <assert_contents>
278 <has_size value="9432" delta="300"/> 278 <has_size value="9639" delta="300"/>
279 </assert_contents> 279 </assert_contents>
280 </output> 280 </output>
281 <output name="output_mapped_reads" ftype="bam"> 281 <output name="output_mapped_reads" ftype="bam">
282 <metadata name="dbkey" value="89"/> 282 <metadata name="dbkey" value="89"/>
283 <assert_contents> 283 <assert_contents>
284 <has_size value="938" delta="100"/> 284 <has_size value="851" delta="100"/>
285 </assert_contents> 285 </assert_contents>
286 </output> 286 </output>
287 </test> 287 </test>
288 <!-- Paired reads in separate datasets, cached reference, output name sorted --> 288 <!-- Paired reads in separate datasets, cached reference, output name sorted -->
289 <test expect_num_outputs="3"> 289 <test expect_num_outputs="3">
292 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/> 292 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/>
293 <param name="output_sort" value="name"/> 293 <param name="output_sort" value="name"/>
294 <output name="output_all_reads" ftype="qname_sorted.bam"> 294 <output name="output_all_reads" ftype="qname_sorted.bam">
295 <metadata name="dbkey" value="89"/> 295 <metadata name="dbkey" value="89"/>
296 <assert_contents> 296 <assert_contents>
297 <has_size value="17103" delta="600"/> 297 <has_size value="17540" delta="600"/>
298 </assert_contents> 298 </assert_contents>
299 </output> 299 </output>
300 <output name="output_unmapped_reads" ftype="qname_sorted.bam"> 300 <output name="output_unmapped_reads" ftype="qname_sorted.bam">
301 <metadata name="dbkey" value="89"/> 301 <metadata name="dbkey" value="89"/>
302 <assert_contents> 302 <assert_contents>
303 <has_size value="17105" delta="600"/> 303 <has_size value="17540" delta="600"/>
304 </assert_contents> 304 </assert_contents>
305 </output> 305 </output>
306 <output name="output_mapped_reads" ftype="qname_sorted.bam"> 306 <output name="output_mapped_reads" ftype="qname_sorted.bam">
307 <metadata name="dbkey" value="89"/> 307 <metadata name="dbkey" value="89"/>
308 <assert_contents> 308 <assert_contents>
309 <has_size value="967" delta="100"/> 309 <has_size value="860" delta="100"/>
310 </assert_contents> 310 </assert_contents>
311 </output> 311 </output>
312 </test> 312 </test>
313 <!-- Collection of Paired reads, history reference, output unsorted --> 313 <!-- Collection of Paired reads, history reference, output unsorted -->
314 <test expect_num_outputs="3"> 314 <test expect_num_outputs="3">
323 <param name="reference" value="NC_002945v4.fasta" dbkey="89" ftype="fasta"/> 323 <param name="reference" value="NC_002945v4.fasta" dbkey="89" ftype="fasta"/>
324 <param name="output_sort" value="unsorted"/> 324 <param name="output_sort" value="unsorted"/>
325 <output name="output_all_reads" ftype="qname_input_sorted.bam"> 325 <output name="output_all_reads" ftype="qname_input_sorted.bam">
326 <metadata name="dbkey" value="89"/> 326 <metadata name="dbkey" value="89"/>
327 <assert_contents> 327 <assert_contents>
328 <has_size value="17059" delta="600"/> 328 <has_size value="17602" delta="600"/>
329 </assert_contents> 329 </assert_contents>
330 </output> 330 </output>
331 <output name="output_unmapped_reads" ftype="qname_input_sorted.bam"> 331 <output name="output_unmapped_reads" ftype="qname_input_sorted.bam">
332 <metadata name="dbkey" value="89"/> 332 <metadata name="dbkey" value="89"/>
333 <assert_contents> 333 <assert_contents>
334 <has_size value="17059" delta="600"/> 334 <has_size value="17602" delta="600"/>
335 </assert_contents> 335 </assert_contents>
336 </output> 336 </output>
337 <output name="output_mapped_reads" ftype="qname_input_sorted.bam"> 337 <output name="output_mapped_reads" ftype="qname_input_sorted.bam">
338 <metadata name="dbkey" value="89"/> 338 <metadata name="dbkey" value="89"/>
339 <assert_contents> 339 <assert_contents>
340 <has_size value="906" delta="100"/> 340 <has_size value="878" delta="100"/>
341 </assert_contents> 341 </assert_contents>
342 </output> 342 </output>
343 </test> 343 </test>
344 </tests> 344 </tests>
345 <help> 345 <help>